<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"> <style>
	.KEYW {color: #933;}
	.COMM {color: #bbb; font-style: italic;}
	.NUMB {color: #393;}
	.STRN {color: #393;}
	.REGX {color: #339;}
	.line {border-right: 1px dotted #666; color: #666; font-style: normal;}
	</style></head><body><pre><span class='line'>  1</span> <span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">prototypeVersionNeeded</span><span class="PUNC">=</span><span class="NUMB">1.7</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>  2</span> </span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">prototypeError</span><span class="PUNC">=</span><span class="STRN">"Prototype "</span><span class="PUNC">+</span><span class="NAME">prototypeVersionNeeded</span><span class="PUNC">+</span><span class="STRN">" has not been loaded!"</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>  3</span> </span><span class="KEYW">try</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>  4</span> </span><span class="WHIT">  </span><span class="NAME">Prototype</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>  5</span> </span><span class="WHIT">  </span><span class="KEYW">if</span><span class="PUNC">(</span><span class="NAME">Prototype.Version</span><span class="PUNC">&lt;</span><span class="NAME">prototypeVersionNeeded</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>  6</span> </span><span class="WHIT">    </span><span class="KEYW">throw</span><span class="PUNC">(</span><span class="STRN">"The version of Prototype ("</span><span class="PUNC">+</span><span class="NAME">Prototype.Version</span><span class="PUNC">+</span><span class="STRN">") is less than the required version, "</span><span class="PUNC">+</span><span class="NAME">prototypeVersionNeeded</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>  7</span> </span><span class="WHIT">  </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'>  8</span> </span><span class="PUNC">}</span><span class="WHIT"> </span><span class="KEYW">catch</span><span class="WHIT"> </span><span class="PUNC">(</span><span class="NAME">e</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'>  9</span> </span><span class="WHIT">  </span><span class="KEYW">throw</span><span class="PUNC">(</span><span class="STRN">"Error: "</span><span class="PUNC">+</span><span class="NAME">prototypeError</span><span class="PUNC">+</span><span class="STRN">"\nAdditionally,\n"</span><span class="PUNC">+</span><span class="NAME">e</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 10</span> </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 11</span> 
<span class='line'> 12</span> 
<span class='line'> 13</span> </span><span class="COMM">// start loading BioJS</span><span class="WHIT">
<span class='line'> 14</span> </span><span class="KEYW">if</span><span class="WHIT"> </span><span class="PUNC">(</span><span class="NAME">Object.isUndefined</span><span class="PUNC">(</span><span class="NAME">Bio</span><span class="PUNC">)</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT"> 
<span class='line'> 15</span>   </span><span class="COMM">/**
<span class='line'> 16</span>    * BioJS
<span class='line'> 17</span>    * @requires PrototypeJS 1.7
<span class='line'> 18</span>    * @version 0.2
<span class='line'> 19</span>    * @author Lee Katz &lt;lskatz@gmail.com>
<span class='line'> 20</span>    * @class The BioJS object
<span class='line'> 21</span>    */</span><span class="WHIT">
<span class='line'> 22</span> </span><span class="WHIT">  </span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">Bio</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT"> </span><span class="PUNC">}</span><span class="PUNC">;</span><span class="WHIT"> 
<span class='line'> 23</span> 
<span class='line'> 24</span> 	</span><span class="COMM">/**
<span class='line'> 25</span> 	 * Values to be used across the board will be stored here
<span class='line'> 26</span> 	 */</span><span class="WHIT">
<span class='line'> 27</span> </span><span class="WHIT">	</span><span class="NAME">Bio.global</span><span class="PUNC">=</span><span class="PUNC">{</span><span class="PUNC">}</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 28</span> </span><span class="WHIT">	
<span class='line'> 29</span> 	</span><span class="COMM">/**
<span class='line'> 30</span> 	 * Bio.global.included stores included files
<span class='line'> 31</span> 	 */</span><span class="WHIT">
<span class='line'> 32</span> </span><span class="WHIT">	</span><span class="NAME">Bio.global.included</span><span class="PUNC">=</span><span class="PUNC">[</span><span class="PUNC">]</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 33</span> 
<span class='line'> 34</span> </span><span class="WHIT">	</span><span class="NAME">scripts</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">$$</span><span class="PUNC">(</span><span class="STRN">"script"</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 35</span> </span><span class="WHIT">  </span><span class="COMM">/**
<span class='line'> 36</span>    * The directory of BioJS (current directory of JS)
<span class='line'> 37</span>    * @see &lt;http://stackoverflow.com/questions/2255689/how-to-get-the-file-path-of-the-currenctly-executing-javascript-code>
<span class='line'> 38</span>    * @field
<span class='line'> 39</span>    * @type String
<span class='line'> 40</span>    */</span><span class="WHIT">
<span class='line'> 41</span> </span><span class="WHIT">	</span><span class="NAME">Bio.global.path</span><span class="PUNC">=</span><span class="NAME">scripts</span><span class="PUNC">[</span><span class="NAME">scripts.length</span><span class="PUNC">-</span><span class="NUMB">1</span><span class="PUNC">]</span><span class="PUNC">.</span><span class="NAME">src</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 42</span> </span><span class="WHIT">	</span><span class="NAME">Bio.global.path</span><span class="PUNC">=</span><span class="NAME">Bio.global.path.replace</span><span class="PUNC">(</span><span class="REGX">/\/Bio.js$/</span><span class="PUNC">,</span><span class="STRN">""</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 43</span> </span><span class="WHIT">	
<span class='line'> 44</span> 	</span><span class="COMM">/**
<span class='line'> 45</span> 	 * Stores all globally used functions for BioJS
<span class='line'> 46</span> 	 * @field
<span class='line'> 47</span> 	 */</span><span class="WHIT">
<span class='line'> 48</span> </span><span class="WHIT">	</span><span class="NAME">Bio.functions</span><span class="PUNC">=</span><span class="PUNC">{</span><span class="PUNC">}</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 49</span> </span><span class="WHIT">  </span><span class="COMM">/**
<span class='line'> 50</span>    * Include a file if it has not already been included.
<span class='line'> 51</span>    * In the style of Perl modules
<span class='line'> 52</span>    * Uses Bio.global.included
<span class='line'> 53</span>    * @function
<span class='line'> 54</span>    * @returns boolean True on success, false if it has already been included or if it didn't work
<span class='line'> 55</span>    */</span><span class="WHIT">
<span class='line'> 56</span> </span><span class="WHIT">  </span><span class="NAME">Bio.functions.include_once</span><span class="PUNC">=</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">module</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 57</span> </span><span class="WHIT">    </span><span class="COMM">// see if it has been included yet</span><span class="WHIT">
<span class='line'> 58</span> </span><span class="WHIT">    </span><span class="KEYW">for</span><span class="PUNC">(</span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">i</span><span class="PUNC">=</span><span class="NUMB">0</span><span class="PUNC">;</span><span class="NAME">i</span><span class="PUNC">&lt;</span><span class="NAME">Bio.global.included.length</span><span class="PUNC">;</span><span class="NAME">i</span><span class="PUNC">++</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 59</span> </span><span class="WHIT">      </span><span class="KEYW">if</span><span class="PUNC">(</span><span class="NAME">Bio.global.included</span><span class="PUNC">[</span><span class="NAME">i</span><span class="PUNC">]</span><span class="PUNC">==</span><span class="NAME">module</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 60</span> </span><span class="WHIT">        </span><span class="KEYW">return</span><span class="WHIT"> </span><span class="KEYW">true</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 61</span> </span><span class="WHIT">      </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 62</span> </span><span class="WHIT">    </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 63</span> </span><span class="WHIT">    </span><span class="COMM">// find the file</span><span class="WHIT">
<span class='line'> 64</span> </span><span class="WHIT">    </span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">path</span><span class="PUNC">=</span><span class="NAME">module.split</span><span class="PUNC">(</span><span class="STRN">'::'</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 65</span> </span><span class="WHIT">    </span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">classFilename</span><span class="PUNC">=</span><span class="NAME">path.pop</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 66</span> </span><span class="WHIT">    </span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">dir</span><span class="PUNC">=</span><span class="NAME">path.join</span><span class="PUNC">(</span><span class="STRN">'/'</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 67</span> </span><span class="WHIT">    </span><span class="NAME">path</span><span class="PUNC">=</span><span class="NAME">Bio.global.path</span><span class="PUNC">+</span><span class="STRN">'/'</span><span class="PUNC">+</span><span class="NAME">dir</span><span class="PUNC">+</span><span class="STRN">'/'</span><span class="PUNC">+</span><span class="NAME">classFilename</span><span class="PUNC">+</span><span class="STRN">'.js'</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 68</span> 
<span class='line'> 69</span> </span><span class="WHIT">    </span><span class="COMM">// include it</span><span class="WHIT">
<span class='line'> 70</span> </span><span class="WHIT">    </span><span class="NAME">document.write</span><span class="PUNC">(</span><span class="STRN">'&lt;script type="text/javascript" src="'</span><span class="WHIT">
<span class='line'> 71</span> </span><span class="WHIT">      </span><span class="PUNC">+</span><span class="WHIT"> </span><span class="NAME">path</span><span class="WHIT"> </span><span class="PUNC">+</span><span class="WHIT"> </span><span class="STRN">'">&lt;/scr'</span><span class="WHIT"> </span><span class="PUNC">+</span><span class="WHIT"> </span><span class="STRN">'ipt>'</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT"> 
<span class='line'> 72</span> 
<span class='line'> 73</span>     </span><span class="COMM">// mark it as included</span><span class="WHIT">
<span class='line'> 74</span> </span><span class="WHIT">    </span><span class="NAME">Bio.global.included.push</span><span class="PUNC">(</span><span class="NAME">module</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 75</span> </span><span class="WHIT">    </span><span class="KEYW">return</span><span class="WHIT"> </span><span class="KEYW">true</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 76</span> </span><span class="WHIT">  </span><span class="PUNC">}</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 77</span> </span><span class="WHIT">	
<span class='line'> 78</span> 	</span><span class="COMM">// include a few classes</span><span class="WHIT">
<span class='line'> 79</span> </span><span class="WHIT">	</span><span class="NAME">Bio.functions.include_once</span><span class="PUNC">(</span><span class="STRN">"Bio::Root"</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT"> </span><span class="COMM">// every class inherits from Root</span><span class="WHIT">
<span class='line'> 80</span> </span><span class="WHIT">	</span><span class="NAME">Bio.functions.include_once</span><span class="PUNC">(</span><span class="STRN">"Bio::SeqIO"</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 81</span> </span><span class="WHIT">	</span><span class="NAME">Bio.functions.include_once</span><span class="PUNC">(</span><span class="STRN">"Bio::IO"</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 82</span> </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 83</span> </span><span class="KEYW">else</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 84</span> </span><span class="WHIT">  </span><span class="KEYW">throw</span><span class="PUNC">(</span><span class="STRN">"Warning: BioJS was has already been loaded, or the Bio variable has already been defined as something else."</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 85</span> </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 86</span> </span></pre></body></html>